PSXII-3 Identification of key metabolic mediators during dietary tryptophan supplementation in low-birth-weight pigs by RNA sequencing

Abstract Low birth weight (LBW) is associated with the development of metabolic syndrome, diabetes mellitus and insulin resistance. While tryptophan (Trp), one of essential amino acids supplied by diet, plays an essential role in fetal growth and development, the effects of Trp supplementation on metabolic processes of postnatal LBW individuals remain unclear. The objective of this study was to identify differentially expressed (DE) genes and altered biological processes in liver of LBW and normal birth weight (NBW) piglets supplemented with Trp. RNA was isolated from liver tissues of three weeks old piglets supplemented with Trp (NBW-0% and LBW-0, 0.4, and 0.8%) and was used for RNA sequencing (RNAseq). There were 100, 191 and 39 DE genes in NBW (N0) and LBW tryptophan 0.4%, 0.8% (L4 and L8) when compared to LBW without Trp supplementation (L0). To determine whether Trp supplementation can resume metabolic regulation-related gene expression to N0 level, DE genes from N0 vs. L0 were clustered into 3 groups based on co-expression trends and clusters were enriched for genes associated with lipid catabolic process, circadian regulation of gene expression and fatty acid response. Further, eight hub genes (PID1, PAFAH2, MAP3K15, ANKRD44, CYP2J34, N4BP2L1, RUSC1 and SALL1) identified in co-expression networks based on Pearson correlation coefficient had strong co-expression coefficients (|r| > 0.9) with each other. In particular, PID1 was significantly associated with many neurological, metabolic, environmental and cardiovascular traits based on phenome-wide association analysis (Phe-WAS). In summary, our study provides novel insights into the molecular mechanism underlying LBW metabolic changes with Trp supplementation in porcine liver tissue and highlights that LBW metabolism restoration may be regulated by genes participating in fatty acid response and cardiovascular diseases.

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Correlation of birth weight with other anthropometric variables in detection of low birth weight (LBW) babies

Journal of Dhaka National Medical College & Hospital ◽

10.3329/jdnmch.v17i1.12189 ◽

2012 ◽

Vol 17 (1) ◽

pp. 29-32 ◽

Cited By ~ 2

Author(s):

Reema Afroza Alia ◽

MA Mannan ◽

Kanij Fatema ◽

Fahmida Begum ◽

Russel Siddique

Keyword(s):

Birth Weight ◽

Low Birth Weight ◽

Observational Study ◽

Pearson Correlation ◽

Calf Circumference ◽

Cross Sectional ◽

Low Birth Weight Babies ◽

Chi Squared ◽

Correlation Tests ◽

Level Of Significance

Objective: To assess the correlation of birth weight with other anthropometric variables and their appropriateness in prediction and detection of low birth weight babies. Methodology: It was a hospital-based cross-sectional observational study, conducted over 100 newborn babies within 24 hours of their birth. Birth weight and other anthropometric variables were recorded and analyzed with statistical package for social science (SPSS-17) and Students t-test, Chi-squared (?2), ANOVA and Pearson correlation tests were done to test the hypothesis and level of significance was set as p <0.05. Result: All the anthropometric variables were well correlated with birth-weight, irrespective of gestational age (p<0.01). The highest correlation was found with chest circumference (r = 0.962), while the lowest correlation was observed with calf circumference (r 0.923). Conclusion: All anthropometric variables except calf circumference can be considered as appropriate indicators for identifying neonates require special attention and intervention for low birth weight (LBW) where weighing machine or facilities for ultrasonography is not readily available. DOI: http://dx.doi.org/10.3329/jdnmch.v17i1.12189 J. Dhaka National Med. Coll. Hos. 2011; 17 (01): 29-32

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Potential Common Key Genes Associated with Chronic Periodontitis and Low Birth Weight: A Case Control Study Using Bioinformatics Analysis of Pooled mRNA Expression Datasets

10.21203/rs.3.rs-35932/v1 ◽

2020 ◽

Author(s):

Asami Suzuki ◽

Tetsuro Horie ◽

Akihito Nakai ◽

Eriko Kikuchi ◽

Yukihiro Numabe

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Birth Weight ◽

Low Birth Weight ◽

Chronic Periodontitis ◽

Web Application ◽

Coiled Coil ◽

Growth Development ◽

Key Genes ◽

Upstream Regulators

Abstract Background: Chronic periodontitis (CP) is a multifactorial disease associated with many systemic diseases. However, the precise association between CP and low birth weight (LBW) remains unclear. Therefore, this study aimed to elucidate common differentially expressed genes (DEGs), biomarker candidates, and upstream regulators related to key genes between CP and LBW.Methods: We investigated molecular relations and biomarker candidates using pooled microarray datasets of CP (GSE12484) and LBW (GSE29807) in the Gene Expression Omnibus (GEO). Datasets were analyzed for common DEGs using GEO2R, an R-based web application for GEO data analysis. Common DEGs, biomarker candidates, and upstream regulators in DEGs between CP and LBW were analyzed using the Database for Annotation Visualization and Integrated Discovery (DAVID), Search Tool for the Retrieval of Interacting Genes (STRING), and QIAGEN’s Ingenuity Pathway Analysis (IPA).Results: Three significantly upregulated and 20 significantly downregulated common DEGs between CP and LBW were identified. Some biological processes and pathways of these downregulated genes were associated with the cell cycle. Biomarker candidates among common DEGs were proline-rich coiled-coil 2A (PPRC2A), topoisomerase (DNA) II alpha (TOP2A), neural cell adhesion molecule 1 (NCAM1), and calcium channel, voltage-dependent, alpha 2/delta subunit 3 (CACNA2D3). Many upstream regulators of these biomarker candidates were factors associated with inflammation, immunity, the cell cycle, and growth development, and were hormones related to pregnancy.Conclusions: The results of this study suggest that PPRC2A, TOP2A, NCAM1, and CACNA2D3 are common biomedical key genes between CP and LBW. The expression states of these genes, which are related to inflammation, hormones, the cell cycle, and growth development, were common in both CP and LBW in blood. To the best of our knowledge, the relations of PPRC2A, TOP2A, and CACNA2D3 to CP and LBW are reported for the first time. Thus, in the bloodstream, inflammatory-related upstream regulators of these key genes may control gene expression associated with fetal growth, and conversely, changes in female hormones due to pregnancy may affect the progress of CP.

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Metabolic regulation of gene expression through histone acylations

Nature Reviews Molecular Cell Biology ◽

10.1038/nrm.2016.140 ◽

2016 ◽

Vol 18 (2) ◽

pp. 90-101 ◽

Cited By ~ 270

Author(s):

Benjamin R. Sabari ◽

Di Zhang ◽

C. David Allis ◽

Yingming Zhao

Keyword(s):

Gene Expression ◽

Metabolic Regulation ◽

Regulation Of Gene Expression

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Triglyceride Configuration and Fat Absorption of Powdered Milk Formulae (Fat and Fatty Acid Balance of the Low Birth Weight Infants Fed on Powdered Milk Formulae Composed of Four Different Amounts of Palmitic Acid at the β-Position of the Triglyceride Molecule)

Pediatrics International ◽

10.1111/j.1442-200x.1979.tb00220.x ◽

1979 ◽

Vol 21 (2) ◽

pp. 34-35

Author(s):

Nooki Kataoka

Keyword(s):

Fatty Acid ◽

Birth Weight ◽

Low Birth Weight ◽

Palmitic Acid ◽

Fat Absorption ◽

Low Birth Weight Infants ◽

Powdered Milk ◽

Triglyceride Molecule

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Omega-3 polyunsaturated fatty acid regulation of gene expression

Current Opinion in Lipidology ◽

10.1097/00041433-200002000-00002 ◽

2000 ◽

Vol 11 (1) ◽

pp. 3-7 ◽

Cited By ~ 142

Author(s):

Pamela T. Price ◽

Carolanne M. Nelson ◽

Steven D. Clarke

Keyword(s):

Gene Expression ◽

Fatty Acid ◽

Polyunsaturated Fatty Acid ◽

Regulation Of Gene Expression ◽

Omega 3

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Regulation of gene expression by DNA methylation with cytotoxic T lymphocytes evaluation in consensus molecular subtypes of colorectal cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.5_suppl.25 ◽

2020 ◽

Vol 38 (5_suppl) ◽

pp. 25-25

Author(s):

Yuanyuan Shen ◽

Justin Hummel ◽

Isabel Cristina Trindade ◽

Christos Papageorgiou ◽

Chi-Ren Shyu ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Dna Methylation ◽

Molecular Subtypes ◽

Epigenetic Modification ◽

Pearson Correlation ◽

Critical Role ◽

Regulation Of Gene Expression ◽

The Cancer Genome Atlas ◽

Highly Correlated

25 Background: Low cytotoxic T lymphocyte (CTLs) infiltration in colorectal cancer (CRC) tumors is a challenge to treatment with immune checkpoint inhibitors. Consensus molecular subtypes (CMS) classify patients based on tumor attributes, and CMS1 patients include the majority of patients with high CTL infiltration and “inflamed” tumors. Epigenetic modification plays a critical role in gene expression and therapy resistance. Therefore, in this study we compared DNA methylation, gene expression, and CTL infiltration of CMS1 patients to other CMS groups to determine targets for improving immunotherapy in CRC. Methods: RNA-seq (n = 511) and DNA methylation (n = 316) from The Cancer Genome Atlas databases were used to determine gene expression and methylation profiles based on CMSs. CMS1 was used as a reference and compared to other subtypes (CMS2-4). Microenvironment Cell Populations- counter (MCPcounter) was used to determine tumor CTL infiltration. Genes with significantly different expression (p < 0.01, LogFC≥|1.5|) and difference of mean methylation β value ≥|0.25| were integrated for Pearson correlation coefficient analysis with MCPcounter score (r > |0.7|). Results: Comparing CMS1 and CMS2, ARHGAP9, TBX21, and LAG3 were differentially methylated and correlated with CTL scores. ARHGAP9 and TBX21 were decreased and hypomethylated in CMS2. Comparing CMS1 and CMS3, ARHGAP9, TBX21, FMNL1, HLA-DPB1, and STX11 were downregulated in CMS3 and highly correlated with CTL scores. ARHGAP9, FMNL1, HLA-DPB1, and STX11 were hypomethylated in CMS3 and TBX21 was methylated in both, but had a higher methylation ratio in CMS1. Comparing CMS1 and CMS4, TBX21 was the only gene downregulated, hypomethylated, and highly correlated with CTL scores in CMS4 patients. Conclusions: We found six genes differentially expressed, differentially methylated, and highly correlated with CTL infiltration when comparing CMS1 to other CMS groups. Specifically, TBX21 was the only gene highly correlated with CTL scores with differential gene expression and methylation in CMS2-4 when compared to CMS1. Thus, T-bet may be a critical regulator of T cell responses in CRC.

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